EP2410332A1 - Methode zur Identifizierung von purinergen Modulatoren des Geruchssystems - Google Patents

Methode zur Identifizierung von purinergen Modulatoren des Geruchssystems Download PDF

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EP2410332A1
EP2410332A1 EP11172539A EP11172539A EP2410332A1 EP 2410332 A1 EP2410332 A1 EP 2410332A1 EP 11172539 A EP11172539 A EP 11172539A EP 11172539 A EP11172539 A EP 11172539A EP 2410332 A1 EP2410332 A1 EP 2410332A1
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atp
receptor
purinergic receptor
agonist
receptors
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Mary Lucero
Colleen Hegg
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University of Utah
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Definitions

  • a longstanding dogma based on lack of efferent synapses, is that odor sensitivity is not modulated at the level of the olfactory receptor neurons (ORNs).
  • ORNs olfactory receptor neurons
  • the sensation of smell occurs in part by the activation of smell receptors present on the ORNs. This activation begins through contact of the chemical signature responsible for the odor with a smell receptor on the ORN.
  • There is a need to be able to modulate sensitivity to smell to for example, decrease sensitivity to smell in noxious environments and increase sensitivity to smell for environments in which it is desirable to smell the odors.
  • compositions and methods relate to the modulation of smell. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive.
  • compositions and methods are not limited to specific synthetic methods, specific recombinant biotechnology methods unless otherwise specified, or to particular reagents unless otherwise specified, as such can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
  • Ranges can be expressed herein as from “about” one particular value, and/or to "about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about,” it will be understood that the particular value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10" is also disclosed.
  • Primers are a subset of probes which are capable of supporting some type of enzymatic manipulation and which can hybridize with a target nucleic acid such that the enzymatic manipulation can occur.
  • a primer can be made from any combination of nucleotides or nucleotide derivatives or analogs available in the art, which do not interfere with the enzymatic manipulation.
  • Probes are molecules capable of interacting with a target nucleic acid, typically in a sequence specific manner, for example through hybridization. The hybridization of nucleic acids is well understood in the art and discussed herein. Typically a probe can be made from any combination of nucleotides or nucleotide derivatives or analogs available in the art.
  • Coapplication is defined as the application of one or more substances simultaneously, such as in the same formulation or consecutively, within a time frame such that each substance is active during a point when the other substance or substances are active.
  • basal levels are normal in vivo levels prior to, or in the absence of, or addition of an agent such as an agonist or antagonist.
  • test compound is defined as any compound to be tested for its ability to interact with a purinergic receptor, e.g., an epithelial Ca 2+ entry channel agonist or antagonist.
  • test components include, for example, drugs, molecules, and compounds that come from combinatorial libraries where thousands of such ligands are screened by drug class.
  • control levels or "control cells” are defined as the standard by which a change is measured, for example, the controls are not subjected to the experiment, but are instead subjected to a defined set of parameters, or the controls are based on pre- or post-treatment levels.
  • compositions disclosed herein have certain functions, such as enhancing or reducing odor sensitivity.
  • Disclosed herein are certain structural requirements for performing the disclosed functions, and it is understood that there are a variety of structures which can perform the same function which are related to the disclosed structures, and that these structures will ultimately achieve the same result, for example stimulation or inhibition of smell.
  • Purinergic nucleotides are important neuromodulators of auditory and visual systems. Disclosed herein is the existence and activity of purinergic receptors in mammalian olfactory epithelium, such as mouse or human, determined through immunohistochemistry, electrophysiology and calcium imaging.
  • P2X and P2Y receptors such as P2Y2, P2X1 and P2X4 immunoreactivity (-IR) was present on the dendrites, soma and axons of olfactory marker protein + (OMP) ORNs, and in the olfactory nerve, glomular and mitral cell layers of the olfactory bulb.
  • OMP olfactory marker protein +
  • P2Y2-IR was observed in the sustentacular cell layer of the epithelium.
  • OE olfactory epithelial
  • AM acetoxymethyl ester
  • Use of selective purinergic receptor agonists demonstrated that P2X and P2Y receptor agonists evoke increases in [Ca 2+ ] i in ORNs with equal frequency and that P2Y but not P2X receptor agonists evoke calcium transients in sustentacular cells.
  • [Ca 2+ ] i levels were measured in response to odor, ATP, or odor + ATP.
  • ATP and ATP analogs modulate odor responses in olfactory receptor neurons.
  • ATP released in the olfactory epithelium following noxious stimuli provides a physiological source for a neuromodulatory substance independent of efferent innervation.
  • Peripheral ATP-mediated odor suppression is a mechanism for reduced olfactory sensitivity during exposure to olfactotoxins.
  • P2X receptors form Ca 2+ -permeable nonselective cation channels that allow Ca 2+ influx from the extracellular fluid.
  • Most of the 8 functional P2Y receptors identified to date act via G-protein coupling to activate phospholipase C, leading to production of inositol triphosphates and mobilization of Ca 2+ from internal stores (Dubyak and el-Moatassim, 1993); however, a few P2Y receptors couple to adenylate cyclase (Ralevic and Burnstock, 1998). All of the components of both transduction pathways have been identified in ORNs (Schild and Restrepo, 1998).
  • purines are odorants for aquatic vertebrates (Kang and Caprio, 1995) and invertebrates ( Carr, W. E., et al., Environ. Health Perspect. 71, 31-46 (1987 )), disclosed herein, extracellular purinergic nucleotides and their receptors in mammalian, such as human, olfactory epithelium exist.
  • mammalian such as human, olfactory epithelium
  • RT-PCR and immunohistochemistry and physiological studies show that sustentacular support cells express P2Y receptors and that ORNs express both P2X and P2Y receptors.
  • Regionally localized purinergic receptors are consistent with extracellular ATP having multiple roles in the peripheral olfactory system.
  • ATP differentially modulates the odor responsiveness of ORNs. This indicates that the complement of P2X and/or P2Y receptor subtypes expressed in the ORN can determine whether the odor response is enhanced or inhibited in the presence of ATP.
  • Adenosine/P1 receptors couple to G proteins and have been further subdivided, based on molecular, biochemical, and pharmacological evidence into four subtypes, A 1 , A 2A , A 2B , and A 3 .
  • P2 receptors divide into two families of ligand-gated ion channels and G protein-coupled receptors termed P2X and P2Y receptors, respectively.
  • Table 1 sets forth seven mammalian P2X receptors (P2X 1-7 ) and five mammalian P2Y receptors (P2Y 1 , P2Y 2 , P2Y 4 , P2Y 6 , P2Y 11 ) which have been cloned and characterized.
  • P2X 1-7 mammalian P2X receptors
  • P2Y 1 , P2Y 2 , P2Y 4 , P2Y 6 , P2Y 11 five mammalian P2Y receptors which have been cloned and characterized.
  • TABLE 1 Families of receptors for purines and pyrimidines (Modified from Ralevic V, Bumstock G.
  • Adenosine/P1 receptors P2 receptors Natural ligands Adenosine ATP, ADP, UTP, UDP, Adenine dinucleotides Subgroup - P2X P2Y Type G protein-coupled Ion channel Nonselective pore G protein-coupled Subtypes A 1 , A 2A , A 2B , A 3 P2X 1-7 , P2X n P2Y 1 , P2Y 2 , P2Y 4 , P2Y 6 , P2Y 11 , P2Y ADP (or P 2T ) Uridine nucleotide-specific
  • P2X receptors are ATP-gated ion channels which mediate rapid (within 10 ms) and selective permeability to cations (Na + , K + and Ca 2+ ) (Bean, 1992; Dubyak and el-Moatassim, 1993; North, 1996). They are typically found on excitable cells (smooth muscle cells, neurons, and glial cells) and mediate fast excitatory neurotransmission to ATP in both the central and peripheral nervous systems. This contrasts with the slower response (less than 100 ms) to ATP acting at metabotropic P2Y receptors, which involves coupling to G proteins and second-messenger systems.
  • P2X 1 to P2X 7 Seven functional P2X receptor proteins (P2X 1 to P2X 7 ) have been cloned and form homomeric ion channels with distinct pharmacological profiles when expressed in Xenopus oocytes (Table 2).
  • the P2X 7 receptor is considered separately below, because it is functionally unique among P2X receptors in being able to act as a non-selective pore.
  • Functional cDNAs encoding the first two members of this family, P2X 1 and P2X 2 were isolated from vas deferens smooth muscle and PC12 pheochromocytoma cells, respectively, using an expression cloning strategy in Xenopus oocytes (Brake et al 1994, Valera et al 1994). In each case, expression of a single cDNA clone in oocytes or transfected mammalian cells is sufficient to direct the synthesis of functional, presumably homomeric ATP-gated ion channel complexes on the surface of these cells.
  • P2X 1 and P2X 2 receptors are clearly related at the level of primary amino acid sequence and predicted secondary structure.
  • P2X proteins that have been cloned are receptor subunits, not actual receptors since a single 2 transmembrane subunit alone cannot form an ion channel.
  • the proteins have 379 to 472 amino acids and are believed to insert into the cell membrane to form a pore comprising two hydrophobic transmembrane domains (M1 and M2), with much of the protein occurring extracellularly as an intervening hydrophilic loop ( figure 8 ). It is presumed that both amino- and carboxyl-termini are located on the intracellular side of the membrane. Based on genetic studies in C.
  • the M2 domain of these channels forms an amphipathic ⁇ -helix whose hydrophilic face lines the pore (Hong & Driscoll 1994).
  • helical wheel plots of M2 domains from each of the cloned P2X subunits show that they have similar potential to form amphipathic ⁇ -helices, despite the limited sequence homology in this region.
  • some P2X subunits contain a region, that resembles the H5 pore loop domain of potassium channels, and it is possible that this segment (just amino-terminal to M2), also contributes to the pore of ATP-gated channels.
  • P2X receptors are believed to form a heterologous complex in biological tissues. Although their subunit stoichiometry is unknown, SDS polyacrylamide gel electrophoresis estimates of the relative molecular mass of the recombinant P2X 1 and P2X 3 receptors determined under non-denaturing conditions (Nicke et al. , 1998) suggest a combination of three subunits (or multiples of three subunits).
  • Both cloned P2X 7 and endogenous P2X 7 -like receptors are unique in that, under physiological conditions they are selectively permeable to small cations only, but in the presence of low divalent cation levels and ATP, the P2X 7 channel can convert to a pore, permeable to small molecules as well as ions.
  • the P2X 7 receptor and its endogenous counterpart is structurally similar to other P2X receptors, except for the fact that it has a significantly longer intracellular C-terminal (240 amino acids) than other P2X receptors, of which at least the last 177 amino acids are crucial for the induction of the non-selective pore (Surprenant et al. , 1996).
  • P2Y receptors are purine and pyrimidine nucleotide receptors that are coupled to G proteins. Most P2Y receptors act via G protein coupling to activate PLC leading to the formation of IP 3 and mobilization of intracellular Ca 2+ . Coupling to adenylate cyclase by some P2Y receptors has also been described. The response time of P2Y receptors is longer than that of the rapid responses mediated by P2X receptors because it involves second-messenger systems and/or ionic conductances mediated by G protein coupling.
  • P2Y 1 , P2Y 2 , P2Y 4 , P2Y 6 , P2Y 11 Five mammalian P2Y receptors (P2Y 1 , P2Y 2 , P2Y 4 , P2Y 6 , P2Y 11 ) have been cloned, and functionally characterized and show distinct pharmacological profiles (Table 3).
  • P2Y receptors are 308 to 377 amino acid proteins with a mass of 41 to 53 kDa after glycosylation.
  • the tertiary structure of P2Y receptors is similar to that of other seven transmembrane domain G protein-coupled receptors ( Figure 9 ).
  • a model of the P2Y receptor based on the primary sequence of the P2Y 1 receptor and using the structural homolog rhodopsin as a G protein-coupled receptor template, has identified positively charged amino acid residues in transmembrane regions 3, 6, and 7 that may be involved in ligand binding by electrostatic interactions with the phosphates of ATP (Van Rhee et al. , 1995) ( Figure 10 ).
  • Extracellular ATP plays an important role in cellular signaling and acts as a cotransmitter or neuromodulator in sensory systems (Thome and Housley, 1996).
  • ATP can be released from synaptic vesicles in trigeminal afferents that innervate the olfactory epithelium and detect noxious chemicals (Finger et al., 1990;Getchell and Getchell, 1992), or via plasma membrane nucleotide transport proteins (Roman et al., 1997).
  • ischemic, stressed, and injured cells release ATP in large amounts.
  • ATP can have autocrine or paracrine effects.
  • Very low concentrations of ATP activate the two subtypes (P2X and P2Y) of purinergic receptors (0.1-10 ⁇ M) (Ralevic and Burnstock, 1998;Schwiebert and Kishore, 2001).
  • P2X and P2Y purinergic receptors
  • ATP is able to stimulate an increase in [Ca 2+ ] i (Illes et al., 2000;Koshimizu et al., 2000;Ralevic and Burnstock, 1998).
  • P2 receptors have broad natural ligand specificity, recognizing ATP, ADP, UTP, UDP, and the diadenosine polyphosphates (Table 1).
  • the chemical structures of some principal P2 receptor agonists and antagonists are illustrated in Figure 11 .
  • P2X selective agonists are the stable ATP analogs ⁇ , ⁇ -meATP and ⁇ , ⁇ -meATP, which if effective, strongly imply actions at P2X receptors (typically at P2X 1 and P2X 3 subtypes) and are generally inactive at P2Y receptors.
  • ADP adenosine 5'-O-(2-thiodiphosphate)(ADP ⁇ S,) and UTP, as these are agonists at some P2Y receptors, but are weak or inactive at P2X receptors.
  • k P2Y 1 and endogenous P2Y 1 -like receptors l P2X 1 , P2X 3 and heteromeric P2X 2 P2X 3 receptors.
  • m P2Y 2 and endogenous P2Y 2 -like receptors and P2Y 4 receptors n P2Y 6 receptor.
  • o P2Y ADP p P2Y 1 and endogenous P2Y 1 -like receptors coupled to AC.
  • AC adenylate cyclase
  • ADP ⁇ F adenosine 5'-O-(2-fluoro)-diphosphate
  • ADP ⁇ S adenosine 5'- O -(2-thio-diphosphate
  • cAMP adenosine 3',5'-cyclic monophosphate
  • A3P5PS adenosine 3'-phosphate 5'-phosphosulfate
  • ATP ⁇ S adenosine 5'-O-(3-thiotriphosphate
  • BzATP 3'- O -(4-benzoyl)benzoyl ATP
  • DAG diacylglycerol
  • DIDS 4,4'-diisothio-cyanatostilbene-2,2'-disulfonate
  • FPL 66096 2-propyl phosphate
  • the P2Y selective agonists UTP and ADP- ⁇ S suppressed the co-application evoked calcium transient indicating they can act as odor suppressants.
  • similar experiments were performed with P2X and P2Y selective agonists giving similar results.
  • compositions and methods for inhibiting the odor response of an ORN are disclosed. Inhibition of the response can be determined by performing the transient calcium flux assays as ,discussed herein. Typically these assays can be performed in the presence or absence of the odor.
  • compositions which inhibit the ORN response can be compositions which in a calcium transient flux assay, the presence of the composition and the odor together, produces a transient calcium flux that is less than the sum of the odor induced flux alone and the composition induced flux alone.
  • compositions that have a ratio of less than or equal to 0.01, 0.03, 0.05, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.52, 0.55, 0.6, 0.64, 0.65, 0.69, 0.7, 0.72, 0.75, 0.80, 0.83, 0.85, 0.87 0.90, 0.92, 0.95, 0.97, or 0.99.
  • the ratio can be expressed in terms of a range of these individual ratios, such as 0.72 to 0.92, for example, or 0.52 to 0.64, or 0.69 to 0.83.
  • P2X selective agonists and P2Y selective agonists Disclosed are P2X directed agonists and P2Y directed agonists.
  • P2X directed agonists and P2Y directed agonists are any agonist that has a greater effect on a P2X receptor than on a P2Y receptor.
  • a P2Y directed agonist is any agonist that has a greater effect on a P2Y receptor than on a P2X receptor.
  • P2X agonists and P2Y agonists can be determined by comparing the activity to known selective agonists, such as those discussed herein. It is understood that the level of activity of each selective agonist discussed herein, is disclosed.
  • P2 agonists that interact with any P2 receptor. It is understood that many P2X and P2Y agonists can be both a selective agonist as well as a directed agonist. For example, UTP can be a selective and a directed P2Y agonist.
  • P2X and P2Y agonists inhibit ORN response to odor stimulants, so too, antagonists of P2X and P2Y receptors can lead to an enhancement of the smell response.
  • P2X antagonists such as those disclosed in Table 4, for example, act at P2X receptors and P2Y antagonists, such as those disclosed in Table 4, for example, act at P2Y receptors, and thus can be stimulators of odor responsiveness. It is understood that the assays, measurements, and functional limitations, as discussed, herein for agonists are applicable for antagonists as well.
  • B an antagonist
  • antagonists have an opposite effect on a receptor than an agonist, and application of the disclosed methods and limitations can be thus applied to antagonists, as they were for agonists.
  • P2X selective antagonists and P2Y selective antagonists Disclosed are P2X selective antagonists and P2Y selective antagonists. Disclosed are P2X directed antagonists and P2Y directed antagonists. In certain embodiments, a P2X directed antagonist is any antagonist that has a greater effect on a P2X receptor than on a P2Y receptor. Likewise, in certain embodiments, a P2Y directed antagonist is any antagonist that has a greater effect on a P2Y receptor than on a P2X receptor. In other embodiments, P2X antagonist and P2Y antagonist can be determined by comparing the activity to known selective antagonists, such as those discussed herein. It is understood that the level of activity of each selective antagonist discussed herein, is disclosed. Also disclosed are P2 antagonists that interact with any P2 receptor. It is understood that many P2X and P2Y antagonists can be both a selective antagonist as well as a directed antagonists.
  • the antagonist can increase the odor sensitivity of the subject, which can be desirable to those with olfactory impairments. Increasing odor sensitivity is also desirable in conjunction with a pleasant smell.
  • the antagonist can reduce basal Ca 2+ levels in olfactory receptor neurons which will make the neurons more excitable during subsequent odor stimulation thereby increasing the odor sensitivity of the subject.
  • the antagonist can increase the ratio of observed coapplication-evoked calcium transient compared to the individual odor peak amplitudes in a cell activation assay, as discussed above.
  • analogs of ATP can be made at the base moiety, the sugar moiety, and the phosphate moiety, as discussed herein.
  • the base moiety can be considered as adenin-9-yl (A).
  • A adenin-9-yl
  • the sugar moiety of a nucleotide is typically a ribose or a deoxyribose.
  • the phosphate moiety of a nucleotide is typically pentavalent phosphate.
  • a non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate), ADP, and ATP.
  • ATP analogs can have modifications to the base moiety which would include natural and synthetic modifications of A, such as hypoxanthin-9-yl (I), and 2-aminoadenin-9-yl, 2-aminoadenine, xanthine, 6-methyl and other alkyl derivatives of adenine, 2-propyl and other alkyl derivatives of adenine, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines, 7-methyladenine, 8-azaadenine, 7-deazaadenine and 3-deazaadenine, and O-6 substituted adenines, including 2-aminopropyladenine.
  • A such as hypoxanthin-9-yl (I), and 2-aminoadenin-9-yl, 2-aminoadenine, xanthine, 6-methyl and other alkyl derivatives of adenine, 2-propyl and other alkyl derivative
  • ATP analogs can also include modifications of the sugar moiety. Modifications to the sugar moiety would include natural modifications of the ribose and deoxy ribose as well as synthetic modifications. Sugar modifications include but are not limited to the following modifications at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C 1 to C 10 , alkyl or C 2 to C 10 alkenyl and alkynyl.
  • 2' sugar modifications also include but are not limited to -O[(CH 2 ) n O] m CH 3 , -O(CH 2 ) n OCH 3 , -O(CH 2 ) n NH 2 , -O(CH 2 ) n CH 3 , - O(CH 2 ) n -ONH 2 , and -O(CH 2 ) n ON[(CH 2 ) n CH 3 )] 2 , where n and m are from 1 to about 10.
  • ATP analogs can have other modifications at the 2' position and include but are not limited to: C 1 to C 10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, and polyalkylamino.
  • Modified sugars would also include those that contain modifications at the bridging ring oxygen, such as CH 2 and S.
  • Nucleotide sugar analogs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
  • sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
  • There are numerous United States patents that teach the preparation of such modified sugar structures such as 4,981,957 ; 5,118,800 ; 5,319,080 ; 5,359,044 ; 5,393,878 ; 5,446,137 ; 5,466,786 ; 5,514,785 ; 5,519,134 ; 5,567,811 ; 5,576,427 ; 5,591,722 ; 5,597,909 ; 5,610,300 ; 5,627,053 ; 5,639,873 ; 5,646,265 ; 5,658,873 ; 5,670,633 ; and 5,700,920 , each of which is herein incorporated by reference in its entirety.
  • ATP analogs can also be modified at the phosphate moiety.
  • Modified phosphate moieties include but are not limited to those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3'-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates.
  • nucleotide analogs need only contain a single modification, but can also contain multiple modifications within one of the moieties or between different moieties.
  • Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.
  • PNA peptide nucleic acid
  • Nucleotide substitutes are nucleotides or nucleotide analogs that have had the phosphate moiety and/or sugar moieties replaced. Nucleotide substitutes do not contain a standard phosphorus atom. Substitutes for the phosphate can be for example, short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
  • morpholino linkages formed in part from the sugar portion of a nucleoside
  • siloxane backbones sulfide, sulfoxide and sulfone backbones
  • formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
  • alkene containing backbones sulfamate backbones
  • sulfonate and sulfonamide backbones amide backbones; and others having mixed N, O, S and CH 2 component parts.
  • Numerous United States patents disclose how to make and use these types of phosphate replacements and include but are not limited to 5,034,506 ; 5,166,315 ; 5,185,444 ; 5,214,134 ; 5,216,141 ; 5,235,033 ; 5,264,562 ; 5,264,564 ; 5,405,938 ; 5,434,257 ; 5,466,677 ; 5,470,967 ; 5,489,677 ; 5,541,307 ; 5,561,225 ; 5,596,086 ; 5,602,240 ; 5,610,289 ; 5,602,240 ; 5,608,046 ; 5,610,289 ; 5,618,704 ; 5,623,070 ; 5,663,312 ; 5,633,360 ; 5,677,437 ; and 5,677,439 , each of which is herein incorporated by reference.
  • non-selective, P2X selective and P2Y selective ATP analogs there are ATP selective agonists and ATP selective antagonists.
  • non-selective purinergic receptor agonists are ATP, ATP ⁇ S, and AMP (Table 4).
  • P2Y-'selective' agonists are UTP, ADP, and MeS-ADP (Table 4).
  • an example of a P2X- ⁇ selective' agonist is ⁇ -methylene ATP (Table 4).
  • Suramin and pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid (PPADS) are examples of non-specific antagonists.
  • homology and identity mean the same thing as similarity.
  • the use of the word homology is used between two non-natural sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences.
  • Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.
  • SEQ ID NO:1 represents a version of a P2X receptor. All fragments of the P2X receptor, as well as the other proteins, such as receptors discussed herein, are considered disclosed.
  • variants of genes and proteins herein disclosed typically have at least, about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence.
  • the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
  • nucleic acids can be obtained by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989 , Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989 , Jaeger et al. Methods Enzymol. 183:281-306, (1989 ) which are herein incorporated by reference for at least material related to nucleic acid alignment. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods can differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity, and be disclosed herein.
  • a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above.
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods.
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80' percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the Needleman and Wunsch calculation method, the Jaeger calculation methods, or any of the other calculation methods.
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).
  • hybridization typically means a sequence driven interaction between at least two nucleic acid molecules, such as a primer or a probe and a gene.
  • Sequence driven interaction means an interaction that occurs between two nucleotides or nucleotide analogs or nucleotide derivatives in a nucleotide specific manner. For example, G interacting with C or A interacting with T are sequence driven interactions. Typically sequence driven interactions occur on the Watson-Crick face or Hoogsteen face of the nucleotide.
  • the hybridization of two nucleic acids is affected by a number of conditions and parameters known to those of skill in the art. For example, the salt concentrations, pH, and temperature of the reaction all affect whether two nucleic acid molecules will hybridize.
  • selective hybridization conditions can be defined as stringent hybridization conditions.
  • stringency of hybridization is controlled by both temperature and salt concentration of either or both of the hybridization and washing steps.
  • the conditions of hybridization to achieve selective hybridization can involve hybridization in high ionic strength solution (6X SSC or 6X SSPE) at a temperature that is about 12-25°C below the Tm (the melting temperature at which half of the molecules dissociate from their hybridization partners) followed by washing at a combination of temperature and salt concentration chosen so that the washing temperature is about 5°C to 20°C below the Tm.
  • the temperature and salt conditions are readily determined empirically in preliminary experiments in which samples of reference DNA immobilized on filters are hybridized to a labeled nucleic acid of interest and then washed under conditions of different stringencies. Hybridization temperatures are typically higher for DNA-RNA and RNA-RNA hybridizations. The conditions can be used as described above to achieve stringency, or as is known in the art. ( Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989 ; Kunkel et al. Methods Enzymol. 1987:154:367, 1987 which is herein incorporated by reference for material at least related to hybridization of nucleic acids).
  • a preferable stringent hybridization condition for a DNA:DNA hybridization can be at about 68°C (in aqueous solution) in 6X SSC or 6X SSPE followed by washing at 68°C.
  • Stringency of hybridization and washing if desired, can be reduced accordingly as the degree of complementarity desired is decreased, and further, depending upon the G-C or A-T richness of any area wherein variability is searched for.
  • stringency of hybridization and washing if desired, can be increased accordingly as homology desired is increased, and further, depending upon the G-C or A-T richness of any area wherein high homology is desired, all as known in the art.
  • selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the limiting nucleic acid is bound to the non-limiting nucleic acid.
  • the non-limiting primer is in for example, 10 or 100 or 1000 fold excess.
  • This type of assay can be performed at under conditions where both the limiting and non-limiting primer are for example, 10 fold or 100 fold or 1000 fold below their K d , or where only one of the nucleic acid molecules is 10 fold or 100 fold or 1000 fold or where one or both nucleic acid molecules are above their K d .
  • selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the primer is enzymatically manipulated under conditions which promote the enzymatic manipulation, for example if the enzymatic manipulation is DNA extension, then selective hybridization conditions would be when at least about 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
  • composition or method meets any one of these criteria for determining hybridization either collectively or singly it is a composition or method that is disclosed herein.
  • nucleic acid based there are a variety of molecules disclosed herein that are nucleic acid based, including for example the nucleic acids that encode, for example the purinergic receptors, as well as various functional nucleic acids.
  • the disclosed nucleic acids are made up of, for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein. It is understood that for example, when a vector is expressed in a cell that the expressed mRNA will typically be made up of A, C, G, and U.
  • an antisense molecule is introduced into a cell or cell environment through for example exogenous delivery, it is advantageous that the antisense molecule be made up of nucleotide analogs that reduce the degradation of the antisense molecule in the cellular environment.
  • a nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage.
  • the base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T).
  • the sugar moiety of a nucleotide is a ribose or a deoxyribose.
  • the phosphate moiety of a nucleotide is pentavalent phosphate.
  • a non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate) or 5'-GMP (5'-guanosine monophosphate).
  • a nucleotide analog is a nucleotide, which contains some type of modification to the base, sugar, or phosphate moieties. Modifications to nucleotides are well known in the art and would include for example, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, and 2-aminoadenine as well as modifications at the sugar or phosphate moieties.
  • Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.
  • PNA peptide nucleic acid
  • conjugates can be chemically linked to the nucleotide or nucleotide analogs.
  • conjugates include but are not limited to lipid moieties such as a cholesterol moiety.
  • a Watson-Crick interaction is at least one interaction with the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute.
  • the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, N1, and C6 positions of a purine based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine based nucleotide, nucleotide analog, or nucleotide substitute.
  • a Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA.
  • the Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.
  • a nucleotide analog is a nucleotide, which contains some type of modification to the base, sugar, or phosphate moieties. Modifications to the base moiety would include natural and synthetic modifications of A, C, G, and T/U as well as different purine or pyrimidine bases, such as uracil-5-yl (.psi.), hypoxanthin-9-yl (I), and 2-aminoadenin-9-yl.
  • a modified base includes but is not limited to 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines
  • Nucleotide analogs can also include modifications of the sugar moiety. Modifications to the sugar moiety would include natural modifications of the ribose and deoxy ribose as well as synthetic modifications. Sugar modifications include but are not limited to the following modifications at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C 1 to C 10 , alkyl or C 2 to C 10 alkenyl and allcynyl.
  • 2' sugar modifications also include but are not limited to -O[(CH 2 ) n O] m CH 3 , -O(CH 2 ) n OCH 3 , -O(CH 2 ) n NH 2 ,-O(CH 2 ) n CH 3 , -O(CH 2 ) n -ONH 2 , and -O(CH 2 ) n ON[(CH 2 ) n CH 3 )] 2 , where n and m are from 1 to about 10.
  • modifications at the 2' position include but are not limited to: C 1 to C 10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.
  • Similar modifications can also be made at other positions on the sugar, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide.
  • Modified sugars would also include those that contain modifications at the bridging ring oxygen, such as CH 2 and S.
  • Nucleotide sugar analogs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
  • Nucleotide analogs can also be modified at the phosphate moiety.
  • Modified phosphate moieties include but are not limited to those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3'-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates.
  • these phosphate or modified phosphate linkage between two nucleotides can be through a 3'-5' linkage or a 2'-5' linkage, and the linkage can contain inverted polarity such as 3'-5' to 5'-3' or 2'-5' to 5'-2'.
  • Various salts, mixed salts and free acid forms are also included.
  • nucleotides containing modified phosphates include but are not limited to, 3,687,808 ; 4,469,863 ; 4,476,301 ; 5,023,243 ; 5,177,196 ; 5,188,897 ; 5,264,423 ; 5,276,019 ; 5,278,302 ; 5,286,717 ; 5,321,131 ; 5,399,676 ; 5,405,939 ; 5,453,496 ; 5,455,233 ; 5,466,677 ; 5,476,925 ; 5,519,126 ; 5,536,821 ; 5,541,306 ; 5,550,111 ; 5,563,253 ; 5,571,799 ; 5,587,361 ; and 5,625,050 , each of which is herein incorporated by reference.
  • nucleotide analogs need only contain a single modification, but can also contain multiple modifications within one of the moieties or between different moieties.
  • Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.
  • PNA peptide nucleic acid
  • Nucleotide substitutes are nucleotides or nucleotide analogs that have had the phosphate moiety and/or sugar moieties replaced. Nucleotide substitutes do not contain a standard phosphorus atom. Substitutes for the phosphate can be for example, short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
  • morpholino linkages formed in part from the sugar portion of a nucleoside
  • siloxane backbones sulfide, sulfoxide and sulfone backbones, formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH 2 component parts.
  • Numerous United States patents disclose how to make and use these types of phosphate replacements and include but are not limited to 5,034,506 ; 5,166,315 ; 5,185,444 ; 5,214,134 ; 5,216,141 ; 5,235,033 ; 5,264,562 ; 5,264,564 ; 5,405,938 ; 5,434,257 ; 5,466,677 ; 5,470,967 ; 5,489,677 ; 5,541,307 ; 5,561,225 ; 5,596,086 ; 5,602,240 ; 5,610,289 ; 5,602,240 ; 5,608,046 ; 5,610,289 ; 5,618,704 ; 5,623,070 ; 5,663,312 ; 5,633,360 ; 5,677,437 ; and 5,677,439 , each of which is herein incorporated by reference.
  • PNA aminoethylglycine
  • United States patents 5,539,082 ; 5,714,331 ;and 5,719,262 teach how to make and use PNA molecules, each of which is herein incorporated by reference. (See also Nielsen et al., Science, 1991, 254, 1497-1500 ).
  • conjugates can be chemically linked to the nucleotide or nucleotide analogs.
  • conjugates include but are not limited to lipid moieties such as a cholesterol moiety ( Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989,86, 6553-6556 ), cholic acid ( Manoharan et al., Bioorg. Med. Chem.
  • a thioether e.g., hexyl-S-tritylthiol ( Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309 ; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770 ), a thiocholesterol ( Oberhauser et al., Nucl.
  • Acids Res., 1990, 18, 3777-3783 a polyamine or a polyethylene glycol chain ( Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973 ), or adamantane acetic acid ( Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654 ), a palmityl moiety ( Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237 ), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety ( Crooke et al., J. Pharmacol. Exp.
  • a Watson-Crick interaction is at least one interaction with the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute.
  • the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, N1, and C6 positions of a purine based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine based nucleotide, nucleotide analog, or nucleotide substitute.
  • a Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA.
  • the Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.
  • compositions including primers and probes, which are capable of interacting with the purinergic receptors as disclosed herein.
  • the primers are used to support DNA amplification reactions.
  • the primers will be capable of being extended in a sequence specific manner.
  • Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer.
  • Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PCR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription. Techniques and conditions that amplify the primer in a sequence specific manner are preferred.
  • the primers are used for the DNA amplification reactions, such as PCR or direct sequencing. It is understood ' that in certain embodiments the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner.
  • the disclosed primers hybridize with a purinergic receptor nucleic acid or region of the purinergic receptor nucleic acid or they hybridize with the complement of the purinergic receptor nucleic acid or complement of a region of the purinergic receptor nucleic acid.
  • compositions and methods which can be used to deliver nucleic acids to cells, either in vitro or in vivo. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems.
  • the nucleic acids can be delivered through a number of direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • the disclosed nucleic acids can be in the form of naked DNA or RNA, or the nucleic acids can be in a vector for delivering the nucleic acids to the cells, whereby the encoding DNA or DNA or fragment is under the transcriptional regulation of a promoter, as would be well understood by one of ordinary skill in the art as well as enhancers.
  • the vector can be a commercially available preparation, such as an adenovirus vector (Quantum Biotechnologies, Inc. (Laval, Quebec, Canada).
  • vector delivery can be via a viral system, such as a retroviral vector system which can package a recombinant retroviral genome (see e.g., Pastan et al., Proc. Natl. Acad. Sci. U.S.A. 85:4486, 1988 ; Miller et al., Mol. Cell. Biol. 6:2895, 1986 ).
  • the recombinant retrovirus can then be used to infect and thereby deliver to the infected cells nucleic acid encoding a broadly neutralizing antibody (or active fragment thereof).
  • the exact method of introducing the altered nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors.
  • adenoviral vectors Mitani et al., Hum. Gene Ther. 5:941-948, 1994
  • AAV adeno-associated viral
  • lentiviral vectors Naidini et al., Science 272:263-267, 1996
  • pseudotyped retroviral vectors Agrawal et al., Exper. Hematol. 24:738-747, 1996 ).
  • compositions and methods can be used in conjunction with any of these or other commonly used gene transfer methods.
  • the dosage for administration of adenovirus to humans can range from about 10 7 to 10 9 plaque forming units (pfu) per injection but can be as high as 10 12 pfu per injection ( Crystal, Hum. Gene Ther. 8:985-1001, 1997 ; Alvarez and Curiel, Hum. Gene Ther. 8:597-613, 1997 ).
  • a subject can receive a single injection, or, if additional injections are necessary, they can be repeated at six-month intervals (or other appropriate time intervals, as determined by the skilled practitioner) for an indefinite period and/or until the efficacy of the treatment has been established.
  • Parenteral administration of the nucleic acid or vector, if used, is generally characterized by injection.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
  • a more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Patent No. 3,610,795 , which is incorporated by reference herein.
  • suitable formulations and various routes of administration of therapeutic compounds see, e.g., Remington: The Science and Practice of Pharmacy (19th ed.) ed. A.R. Gennaro, Mack Publishing Company, Easton, PA 1995 .
  • Nucleic acids that are delivered to cells which are to be integrated into the host cell genome typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used. These viral integration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid based system of deliver, such as a liposome, so that the nucleic acid contained in the delivery system can be come integrated into the host genome.
  • Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome. These systems and the methods necessary to promote homologous recombination are known to those of skill in the art.
  • compositions can be delivered to the target cells in a variety of ways.
  • the compositions can be delivered through electroporation, or through lipofection, or through calcium phosphate precipitation.
  • the delivery mechanism chosen will depend in part on the type of cell targeted and whether the delivery is occurring for example in vivo or in vitro.
  • compositions can comprise, in addition to the disclosed compositions or vectors for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, DC-cholesterol) or anionic liposomes.
  • liposomes can further comprise proteins to facilitate targeting a particular cell, if desired.
  • Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract.
  • liposomes see, e.g., Brigham et al. Am. J. Resp. Cell. Mol. Biol. 1:95-100 (1989 ); Felgner et al.
  • the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage.
  • delivery of the compositions to cells can be via a variety of mechanisms.
  • delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, MD), SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison, WI), as well as other liposomes developed according to procedures standard in the art.
  • nucleic acid or vector can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, CA) as well as by means of a SONOPORATION machine (ImaRx Pharmaceutical Corp., Arlington, AZ).
  • the materials can be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These can be targeted to a particular cell type via antibodies, receptors, or receptor ligands.
  • the following references are examples of the use of this technology to target specific proteins to tumor tissue ( Senter, et al., Bioconjugate Chem., 2:447-451, (1991 ); Bagshawe, K.D., Br. J. Cancer, 60:275-281, (1989 ); Bagshawe, et al., Br. J. Cancer, 58:700-703, (1988 ); Senter, et al., Bioconjugate Chem., 4:3-9, (1993 ); Battelli, et al., Cancer Immunol.
  • the internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis have been reviewed ( Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991 )).
  • compositions can be administered in a pharmaceutically acceptable carrier and can be delivered to the subject's cells in vivo and/or ex vivo by a variety of mechanisms well known in the art (e.g., uptake of naked DNA, liposome fusion, intramuscular injection of DNA via a gene gun, endocytosis and the like).
  • cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art.
  • the compositions can be introduced into the cells via any gene transfer mechanism, such as, for example, calcium phosphate mediated gene delivery, electroporation, microinjection or proteoliposomes.
  • the transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.
  • the nucleic acids that are delivered to cells typically contain expression-controlling systems.
  • the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product.
  • a promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site.
  • a promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and can contain upstream elements and response elements.
  • Preferred promoters controlling transcription from vectors in mammalian host cells can be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter.
  • viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter.
  • the early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication ( Fiers et al., Nature, 273: 113 (1978 )).
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a Hin dIII E restriction fragment ( Greenway, P.J. et al., Gene 18: 355-360 (1982 )).
  • promoters from the host cell or related species also are useful herein.
  • Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5' ( Laimins, L. et al., Proc. Natl. Acad. Sci. 78: 993 (1981 )) or 3' ( Lusky, M.L., et al., Mol.Cell Bio. 3:1108 (1983 )) to the transcription unit. Furthermore, enhancers can be within an intron ( Banerji, J.L. et al., Cell 33:729 (1983 )) as well as within the coding sequence itself ( Osborne, T.F., et al., Mol. Cell Bio. 4:1293 (1984 )).
  • Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, -fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the promoter and/or enhancer can be specifically activated either by light or specific chemical events which trigger their function.
  • Systems can be regulated by reagents such as tetracycline and dexamethasone.
  • reagents such as tetracycline and dexamethasone.
  • irradiation such as gamma irradiation, or alkylating chemotherapy drugs.
  • the promoter and/or enhancer regions can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed.
  • the promoter and/or enhancer region be active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time.
  • a preferred promoter of this type is the CMV promoter (650 bases).
  • Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTF.
  • GFAP glial fibrillary acetic protein
  • Expression vectors used in eukaryotic host cells can also contain sequences necessary for the termination of transcription which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contains a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA.
  • polyadenylation signals in expression constructs are well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs.
  • the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases. It is also preferred that the transcribed units contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct.
  • the vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed.
  • Preferred marker genes are the E . coli lacZ gene, which encodes ⁇ -galactosidase, and green fluorescent protein.
  • the marker can be a selectable marker.
  • suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin.
  • DHFR dihydrofolate reductase
  • thymidine kinase thymidine kinase
  • neomycin neomycin analog G418, hydromycin
  • puromycin puromycin.
  • selectable markers When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure.
  • These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media.
  • An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non-supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, ( Southern P. and Berg, P., J. Molec. Appl. Genet. 1:327 (1982 )), mycophenolic acid, ( Mulligan, R.C. and Berg, P. Science 209:1422 (1980 )) or hygromycin, ( Sugden, B. et al., Mol. Cell. Biol. 5:410-413 (1985 )).
  • the three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puromycin.
  • Protein variants and derivatives are well understood to those of skill in the art and in can involve amino acid sequence modifications.
  • amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants.
  • Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues.
  • Immunogenic fusion protein derivatives are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion.
  • Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule.
  • These variants ordinarily are prepared by site-specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture.
  • substitution mutations at predetermined sites in DNA having a known sequence are well known, for example M13 primer mutagenesis and PCR mutagenesis.
  • Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues.
  • Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a final construct.
  • the mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure.
  • Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Tables 5 and 6 and are referred to as conservative substitutions.
  • substitutions that are less conservative than those in Table 6, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain.
  • the substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g.
  • an electropositive side chain e.g., lysyl, arginyl, or histidyl
  • an electronegative residue e.g., glutamyl or aspartyl
  • substitutions include combinations such as, for example, Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
  • substitutions include combinations such as, for example, Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
  • Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein.
  • Substitutional or deletional mutagenesis can be employed to insert sites for N-glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr).
  • Deletions of cysteine or other labile residues also can be desirable.
  • Deletions or substitutions of potential proteolysis sites, e.g. Arg is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues.
  • Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Other post-translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o-amino groups of lysine, arginine, and histidine side chains ( T.E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco pp 79-86 [1983 ]), acetylation of the N-terminal amine and, in some instances, amidation of the C-terminal carboxyl.
  • variants and derivatives of the disclosed proteins herein are through defining the variants and derivatives in terms of homology/identity to specific known sequences.
  • SEQ ID NO:1 sets forth a particular sequence of a P2X receptor.
  • variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the stated sequence.
  • the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
  • nucleic acids can be obtained by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989 , Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989 , Jaeger et al. Methods Enzymol. 183:281-306, 1989 which are herein incorporated by reference for at least material related to nucleic acid alignment.
  • nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e. all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences. Thus, while each particular nucleic acid sequence cannot be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequence.
  • compositions such as the ATP and ATP analogs
  • pharmaceutically acceptable is meant a material that is not biologically or otherwise undesirable, i.e., the material can be administered to a subject, along with the nucleic acid or vector, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.
  • the carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
  • compositions can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including topical intranasal administration or administration by inhalant.
  • topical intranasal administration means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the composition.
  • Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation.
  • compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the allergic disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
  • Parenteral administration of the composition is generally characterized by injection.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
  • a more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Patent No. 3,610,795 , which is incorporated by reference herein.
  • the materials can be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These can be targeted to a particular cell type via antibodies, receptors, or receptor ligands.
  • the following references are examples of the use of this technology to target specific proteins to tumor tissue ( Senter, et al., Bioconjugate Chem., 2:447-451, (1991 ); Bagshawe, K.D., Br. J. Cancer, 60:275-281, (1989 ); Bagshawe, et al., Br. J. Cancer, 58:700-703, (1988 ); Senter, et al., Bioconjugate Chem., 4:3-9, (1993 ); Battelli, et al., Cancer Immunol.
  • Vehicles such as "stealth” and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo.
  • the internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis have been reviewed ( Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991 )).
  • Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A.R. Gennaro, Mack Publishing Company, Easton, PA 1995 .
  • an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic.
  • the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution.
  • the pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5.
  • Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers can be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.
  • compositions can be administered intramuscularly or subcutaneously. Other compounds will be administered according to standard procedures used by those skilled in the art.
  • compositions can include carriers, thickeners, diluents, buffers, preservatives, surface-active agents and the like in addition to the molecule of choice.
  • Pharmaceutical compositions can also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents, anesthetics, and the like.
  • the pharmaceutical composition can be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration can be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection.
  • the disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.
  • Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions.
  • non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives can also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
  • Formulations for topical administration can include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders.
  • Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like can be necessary or desirable.
  • compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders can be desirable.
  • compositions can potentially be administered as a pharmaceutically acceptable acid- or base- addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid
  • organic acids such as formic acid, acetic acid, propionic acid, glyco
  • Effective dosages and schedules for administering the compositions can be determined empirically, and making such determinations is within the skill in the art.
  • the dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms of the disorder are affected.
  • the dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like.
  • the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art.
  • the dosage can be adjusted by the individual physician in the event of any counterindications. Dosage can vary, and can be administered in one or more dose administrations hourly or daily,for one or several days.
  • a typical daily dosage of the ATP or ATP analogs used alone might range from about 1 ⁇ g/kg to up to 100 mg/kg of body weight or more per day, depending on the factors mentioned above. For example, based on the similarities of EC 50 concentrations for P2 receptors across many species an effective dose to modulate smell in a human would be similar to our mouse model, i.e.,10-200 ⁇ M.
  • compositions disclosed herein are efficacious in modulating, such as enhancing or reducing the sensation of smell in a subject, by observing that the composition reduces or enhances the sensation of smell to a particular or general odor stimulant.
  • Smell sensation can be measured by methods that are known in the art, for example, and in vitro methods using an ORN calcium imaging assay as discussed herein, can also be used.
  • compositions that modulate smell disclosed herein can be administered prophylactically to patients or subjects who are at risk for being exposed to severe or damaging odor stimulation or who have a desire to have either an increased or decreased sensitivity to an odor.
  • elderly people can increase sensitivity to odor to compensate for loss during aging.
  • those on chemotherapy drugs may need decreased odor sensitivity to reduce nausea.
  • nucleic acids and proteins and compositions can be represented as a sequence consisting of the nucleotides of amino acids.
  • the nucleotide guanosine can be represented by G or g.
  • the amino acid valine can be represented by Val or V.
  • chips where at least one address is the sequences or part of the sequences set forth in any of the nucleic acid sequences disclosed herein. Also disclosed are chips where at least one address is the sequences or portion of sequences set forth in any of the peptide sequences disclosed herein. Disclosed are chips where at least one address is the composition, such as an ATP analog, disclosed herein.
  • chips where at least one address is a variant of the sequences or part of the sequences set forth in any of the nucleic acid sequences disclosed herein. Also disclosed are chips where at least one address is a variant of the sequences or portion of sequences set forth in any of the peptide sequences disclosed herein.
  • kits that are drawn to reagents that can be used in practicing the methods disclosed herein.
  • the kits can include any reagent or combination of reagent discussed herein or that would be understood to be required or beneficial in the practice of the disclosed methods.
  • the kits could include an ATP analog in a formulation for delivery to an ORN.
  • a kit for modulating odor sensitivity comprising ATP in a formulation for delivery to an ORN.
  • compositions disclosed herein and the compositions necessary to perform the disclosed methods can be made using any method known to those of skill in the art for that particular reagent or compound unless otherwise specifically noted.
  • the disclosed ATP analogs can be made using a variety of synthetic procedures. Often the analogs can be purchased. For example, the following analogs can be purchased from Sigma Inc., 2-(Methylthio)adenosine 5'-triphosphate, 2-Chloroadenosine 5' triphosphate, 2',5'-Dideoxyadenosine 3'-triphosphate, 2'-3'-O-(4-Benzoylbenzoyl)adenosine 5'-triphosphate, 2'-Monophosphoadenosine 5'-diphosphoribose, ATP-Ribose, 8-Bromoadenosine 5'-triphosphate, Adenosine 5'-triphosphate P3-[1-(2-nitrophenyl)ethyl ester] (Caged ATPNPE caged ATP), Adenosine 5'-triphosphate, Adenosine 5'-( ⁇ , ⁇ -imido)triphosphate, A
  • the nucleic acids such as, the oligonucleotides to be used as primers can be made using standard chemical synthesis methods or can be produced using enzymatic methods or any other known method. Such methods can range from standard enzymatic digestion followed by nucleotide fragment isolation (see for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989) Chapters 5, 6 ) to purely synthetic methods, for example, by the cyanoethyl phosphoramidite method using a Milligen or Beckman System 1Plus DNA synthesizer (for example, Model 8700 automated synthesizer of Milligen-Biosearch, Burlington, MA or ABI Model 380B).
  • a Milligen or Beckman System 1Plus DNA synthesizer for example, Model 8700 automated synthesizer of Milligen-Biosearch, Burlington, MA or ABI Model 380B.
  • compositions can be used in a variety of ways as research tools.
  • the disclosed compositions such as ATP and analogs, can be used to study the signal transduction pathways related to olfactory signaling.
  • compositions can be used as discussed herein as either reagents in micro arrays or as reagents to probe or analyze existing microarrays.
  • the compositions can also be used in any known method of screening assays, related to chip/micro arrays.
  • the compositions can also be used in any known way of using the computer readable embodiments of the disclosed compositions, for example, to study relatedness or to perform molecular modeling analysis related to the disclosed compositions.
  • kits for screening for an agonist or an antagonist of purinergic receptor of the olfactory system comprising contacting a purinergic receptor with a test compound; detecting intracellular calcium levels; and screening for a change in calcium levels as compared to a control level, a change indicating the compound is an agonist or an antagonist of the olfactory system.
  • Multi-well plates are standard in the art and come in a variety of sizes and shapes.
  • the multi-well plate can be 24, 48, or 96 well plates.
  • Such screening assays can be automated or further modified for high throughput analysis.
  • each well can include numerous test components. If a positive reaction is detected in a well, the screening is repeated with one of the test compounds contained in a single well.
  • An “elevation in calcium” is defined as an increase in calcium levels greater than 1 nM above basal levels.
  • the change in calcium levels can be between 5 nM and 10 nM, for example.
  • the elevation in calcium can also be greater than 100 nM above basal levels.
  • a “transient reduction in calcium” is defined as decrease in calcium levels greater than 1 nM below basal levels.
  • the reduction in calcium can also be greater than 100 nM below basal levels.
  • transient means not permanent. Thus, transient can be less than 10 seconds, less than 30 seconds, less than 1 minute, less than 5 minutes, less than 10 minutes, or less than 20 minutes, for example.
  • sustained means that the effect continues for a period of tim.
  • sustained can be greater than 1 minute, greater than 5 minutes, greater than 10 minutes, greater than an hour, greater than 24 hours, or greater than 1 year.
  • Also disclosed is a method of screening for an agonist or an antagonist of a purinergic receptor of the olfactory system comprising contacting a first purinergic receptor expressing cell with a set of test compounds; detecting calcium levels in the first purinergic receptor cell; and selecting each compound in the set that contacted the first purinergic receptor cell, wherein the first purinergic receptor cell showed a transient change in calcium as compared to a control level, indicating the compound is an agonist or an antagonist of a purinergic receptor of the olfactory system.
  • the method can further comprise the steps of contacting a second purinergic receptor cell with one test compound selected above, and detecting calcium levels in the second purinergic receptor cell, wherein a transient change in calcium as compared to a control level indicates the compound is an agonist or an antagonist of a purinergic receptor of the olfactory system.
  • Also disclosed is a method of screening for an agonist or an antagonist of a purinergic receptor of the olfactory system comprising contacting a test compound with a cell that expresses a heterologous nucleic acid that encodes a purinergic receptor; and detecting calcium levels in the cell; a transient change in calcium as compared to a control level, indicating an agonist or an antagonist of a purinergic receptor of the olfactory system.
  • agents identified by the screening methods described herein as well as methods of making those agents.
  • An example of a method of making an agent includes identifying the agent using the methods provided herein, and manufacturing the agent or manufacturing the agent in a pharmaceutically acceptable carrier.
  • the cell is a cell that lacks the receptor prior to introduction of the heterologous nucleic acid.
  • the cell can be transiently transfected with the heterologous nucleic acid or a stable cell line containing the expressed receptor can be made using standard techniques in the art.
  • heterologous nucleic acid is meant that any heterologous or exogenous nucleic acid can be inserted into a vector for transfer into a cell, tissue or organism.
  • the nucleic acid can encode a polypeptide or protein or an antisense RNA, for example.
  • the nucleic acid can be functionally linked to a promoter.
  • the promoter can promote expression of the heterologous nucleic acid, as is known in the art, such as appropriate orientation of the promoter relative to the heterologous nucleic acid.
  • the heterologous nucleic acid preferably has all appropriate sequences for expression of the nucleic acid, as known in the art, to functionally encode, i.e., allow the nucleic acid to be expressed.
  • the nucleic acid can include, for example, expression control sequences, such as an enhancer, and necessary information processing sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites, and transcriptional terminator sequences.
  • Calcium levels and changes in calcium levels can be detected using a calcium indicator such as the cell-permeable methyl ester form of Fura-2, which is Fura-2/AM.
  • a fluorescence plate reader is used that detects a single wavelength, such as Ca 2+ indicator dyes Fluo 3, Fluo 4 AM, Quin 2, Indo-1 and Indo-4.
  • the compound being screened can augment the effects of other compounds such as ATP, for example.
  • the compound being screened can be tested in the presence of another compound that stimulates the purinergic receptor.
  • the purinergic receptor expressing cell can be in a solution containing an effective amount of ATP.
  • An "effective amount of ATP" is defined as about 300 nM to about 1 mM of ATP.
  • Example 1 ATP differentially modulates odor responsiveness through purinergic receptor activation: activation of purinergic receptor subtypes differentially modulates odor sensitivity
  • RT-PCR and immunohistochemical methods ionotropic P2X 2 and G-protein-coupled P2Y 2 receptor expression were found in both olfactory epithelium and olfactory bulb.
  • RT-PCR analysis revealed mRNA expression for the P2Y 2 receptor and two isoforms of the P2X 2 receptor; P2X 2-1 ( Brake, A. J., et al., Nature 371, 519-523 (1994 )) and P2X 2-2 (Brandle et al., 1997) ( Fig. 1A ).
  • OMP olfactory marker protein
  • Both P2X- and P2Y-IR was absent from dendritic knobs and cilia of ORNs.
  • OMP-negative ORNs and basal cells olfactory stem cells
  • Sustentacular cells and Bowman's glands showed only P2Y 2 -IR (Fig 1D).
  • P2X 1 , P2X 2 , P2X 4 and P2Y 2 receptor IR in the olfactory nerve layer, the glomerular layer and the mitral cell layer.
  • the underlying blood vessels are the likely source of P2X 2 mRNA identified by the RT-PCR studies of the olfactory epithelium.
  • Preabsorption of the primary antibody with peptide antigen (Fig. 1E) or omission of the primary antibody blocked the purinergic receptor staining.
  • Identification of regionally localized purinergic receptors in mammalian olfactory epithelium is consistent with extracellular ATP playing multiple roles in the peripheral olfactory system.
  • purinergic receptor agonists were used. As there are no completely specific purinergic receptor agonists (Ralevic and Burnstock, 1998), the selectivity was determined as discussed herein.
  • the P2X 'selective' agonist ⁇ -methylene ATP was superfused onto the slice ( Fig. 3C ). Only the ORNs, and not the sustentacular cells, responded to ⁇ -methylene ATP with an increase in [Ca 2+ ] i ( Fig. 3C5 ).
  • the P2Y 'selective' agonist UTP evoked calcium transients in both ORNs and sustentacular cells ( Fig.
  • ATP non-selective purinergic receptor agonists
  • P2Y-'selective' agonists UDP, ADP, MeS-ADP
  • P2X-'selective' agonists ⁇ methylene ATP
  • adenosine an adenosine receptor 'selective' agonist
  • ORNs responded with approximately equal frequency to P2Y and P2X receptor agonists whereas sustentacular cells responded primarily to P2Y receptor agonists.
  • the general non-specific purinergic receptor antagonists Suramin and pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid (PPADS) were used to further confirm that purinergic-evoked calcium transients were mediated via purinergic receptors.
  • PPADS pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid
  • Purinergic receptor antagonists also reversibly blocked purinergic nucleotide-evoked calcium transients in sustentacular cells.
  • ⁇ -methylene ATP like ATP, enhanced the odor responsiveness due to the activation of P2X receptors in a few cells.
  • the P2X specific agonist significantly reduced odor-induced Ca 2+ transients.
  • purinergic receptor subtypes are differentially expressed in ORNs and sustentacular cells, and ORNs express multiple purinergic receptor subtypes.
  • expression of more than one type of purinergic receptor allows for regulation of multiple effectors and modification of agonist-evoked responses, and provides a mechanism for rapid and local fine tuning at the cellular level (Ralevic and Burnstock, 1998).
  • Disclosed immunohistochemical studies showed a notable absence of purinergic receptors in the dendritic knobs and cilia, the site of odor transduction, whereas both P2X and P2Y receptors are located on cell somas and other regions.
  • Primers for detection of P2X 2 transcripts were 756-775 sense and 1537-1558 antisense oligonucleotides (accession #U14414)(Brake et al., 1994), primers for P2Y 2 transcripts were 1288-1307 sense and 1931-1950 antisense oligonucleotides (accession #U09402), primers for ⁇ -actin transcripts (Lopez-Candales et al., 1995) were 1038-1067 sense and 1875-1905 antisense oligonucleotides and primers for neuron specific enolase were 348-368 sense and 1101-1123 antisense oligonucleotides (accession #M11931).
  • PCR products were separated and visualized using ethidium bromide-stained agarose gels (1%). A semi-nested PCR protocol was used for detection of the P2X 2 receptor transcript. PCR products were excised from the gel and reamplified for 28 cycles using the same antisense primer and a sense primer corresponding to position 1059-1078. PCR products were sequenced at the University of Utah Sequencing Center.
  • mice postnatal day 0-6 were quickly decapitated, and the skin and lower jaw were removed. Tissue was mounted in ice cold Ringers onto a vibratome-cutting block and 300 ⁇ m slices were made. Primary cultures of mouse ORNs were made using the same protocol and culture conditions as described for rat olfactory receptor neurons (Vargas and Lucero, 1999a). Briefly, tissue was placed in divalent cation-free Ringers containing 10 mg/ml bovine serum albumin, 1 mg/ml deoxyribonuclease II and 44 U/ml dispase, incubated at 37°C for 45 min.
  • tissue was washed, triturated, and filtered through a 53 mm mesh and 200 ml cells were plated onto concanavalin A-coated coverslips and allowed to settle for 20 min.
  • An additional 1.5 ml of culture medium was added (DMEM supplemented with 100 mM ascorbic acid, 1X insulin-transferrin-seleniumX (GIBCO BRL), 2 mM glutamine, 100 U/ml penicillin G and 100 mg/ml streptomycin).
  • Electrodes (2 -5 M ⁇ ) were filled with TMA-oxide internal solution (in mM: 62.5 TMA oxide, 62.5 KH 2 PO 4 , 15 KCl, 5 MgCl 2 , 11 EGTA, 10 HEPES, 1 glutathione, 5 TEA, 0.03% pluronic acid F-127, 0.3% DMSO, 150 mg/ml nystatin, pH 7.2, 330 mOsm).
  • TMA-oxide internal solution in mM: 62.5 TMA oxide, 62.5 KH 2 PO 4 , 15 KCl, 5 MgCl 2 , 11 EGTA, 10 HEPES, 1 glutathione, 5 TEA, 0.03% pluronic acid F-127, 0.3% DMSO, 150 mg/ml nystatin, pH 7.2, 330 mOsm).
  • Electro-olfactogram and on-cell recordings Slices of P0-P6 mouse OE were prepared as described above and mounted in a perfusion chamber with a bath flow of 3 ml/min. Test chemicals were introduced using a rotary injection valve (Rheodyne, Cotati, CA).
  • the electro-olfactogram (EOG) recording electrode (3 M NaCl in1%agar; tip diameter, 5-10 um) was positioned along the dorsal portion of the nasal septum.
  • the differential electrode (identical to the recording electrode) was positioned over skull cartilage and an Ag 2 /AgCl 2 ground electrode was connected to the bath solution via a 3 M KCl agar bridge.
  • Responses to test agents were amplified (5000 X gain) and filtered (2 kHz) by a low-noise differential DC amplifier. Data was digitized (100 Hz) using Axoscope 8.0 software (Axon Instruments).
  • the electrode was lowered into the dorsal septal region of the slice and a seal (0.5-1 Gohms) was made in voltage-clamp before switching to currentclamp with zero applied current. Only cells with a stable baseline were used. There was a 7 min wash between each test application. Experiments were conducted on 65 cells in 42 slices obtained from 14 P0-P6 mice from three litters. Only three cells survived long enough to complete the recovery portion of the >27 min protocol.
  • [Ca 2+ ] i was determined using confocal imaging of fluo-4 AM (18 ⁇ M; Molecular Probes) loaded cells and slices.
  • Cells or slices were placed in a laminar flow chamber (Warner Instruments) and perfused continuously with Ringers solution at a flow rate of 1.5-2.0 ml/min.
  • Ringers contained (mM): 140 NaCl, 5 KCl, 1MgCl 2 , 2 CaCl 2 , 10 HEPES, 10 glucose, 500 probenicid and 400 nM tetrodotoxin.
  • Test solutions were applied using bath exchange and a small volume loop injector (200 ⁇ l).
  • a Zeiss LSM 510 confocal laser scanning system was used for data collection and analysis.
  • Example 3 ATP Reduces Cyclic Nucleotide-Induced Electrical Responses
  • Odor activation of G-protein-coupled receptors results in increased cAMP production, opening of cyclic nucleotide-gated channels, influx of Ca 2+ and Na + , depolarization of the membrane, and activation of voltage- and Ca 2+ -gated ion channels (Schild and Restrepo,1998).
  • purinergics can reduce the odor-evoked electrical activity of ORNs. Recording odor-evoked membrane responses from single ORNs has a low probability of success because each ORN expresses only one or a few odorant receptors (Buck and Axel, 1991).
  • a mixture of cyclic nucleotide modulators were used to record membrane responses: IBMX (100 ⁇ M), a phosphodiesterase inhibitor that prevents the breakdown of cAMP, CPT-cAMP (50 ⁇ M), and 8-Br-cGMP (50 ⁇ M), both membrane-permeant analogs of cAMP and cGMP, respectively.
  • This cyclic nucleotide mixture was tested initially to verify that it evoked membrane potential changes in the OE slice preparation.
  • the EOG measures field potential changes across the OE after stimulation. Similar EOG responses were obtained from both odor (10 ⁇ M) and the cyclic nucleotide mixture ( Fig. 13A ), validating the replacement of odor with the mixture in subsequent recordings.
  • SEQ ID NO:1 The following is the sequence for H.sapiens mRNA for ATP receptor P2X1 (accession number X83688). Other sequences have been published for P2X1 receptors from rat vas deferens (accession number X80477) and mouse urinary bladder (accession number X84896).
  • SEQ ID NO:2 The following is the sequence for H.sapiens protein for ATP receptor P2X1 (accession number X83688).
  • SEQ ID NO:3 The following sequence for the P2X2 receptor is derived from rat PC12 cells (accession number U14414). Other sequences have been published for P2X2 receptors from rat cerebellum (accession number Y09910)
  • SEQ ID NO:4 The following sequence for the P2X2 receptor is derived from rat PC12 cells (accession number U14414) protein sequence.
  • SEQ ID NO:5 The following sequence for the P2X3 receptor is derived from H.sapiens (accession number Y07683). Other sequences have been published for P2X3 receptors from rat dorsal root ganglion (accession number X91167 and X90651).
  • SEQ ID NO:6 The following sequence for the P2X3 receptor is derived from H.sapiens (accession number Y07683) protein sequence.
  • SEQ ID NO:7 The following sequence for the P2X4 receptor is derived from H.sapiens (accession number Y07684). Other sequences have been published for P2X4 receptors from rat brain (accession number X93565, U32497, X91200 and X87763) and rat pancreatic islet (accession number U47031).
  • SEQ ID NO:8 The following sequence for the P2X4 receptor is derived from H.sapiens (accession number Y07684) Protein sequence.
  • SEQ ID NO:9 The following sequence for the P2X5 receptor is derived from H.sapiens (accession number AF016709). Other sequences have been published for P2X5 receptors from rat brain (accession number X92069) and rat heart (accession number X97328).
  • SEQ ID NO:10 The following sequence for the P2X5 receptor is derived from H.sapiens (accession number AF016709) protein sequence.
  • SEQ ID NO:11 The following sequence for the P2X6 receptor is derived from H.sapiens (accession number AF065385). Other sequences have been published for P2X6 receptors from rat brain (accession numbers X92070 and X97376).
  • SEQ ID NO:12 The following sequence for the P2X6 receptor is derived from H.sapiens (accession number AF065385) protein sequence.
  • SEQ ID NO:13 The following sequence for the P2X7 receptor is derived from H.sapiens brain (accession number Y09561). Please note that other sequences have been published for P2X7 receptors from rat brain (accession numbers X95882)
  • SEQ ID NO:14 The following sequence for the P2X7 receptor is derived from H.sapiens brain (accession number Y09561) protein sequence
  • SEQ ID NO:15 The following sequence for the P2Y1 receptor is derived from H.sapiens (accession number S81950). Other sequences have been published for P2Y1 receptors from human placenta (accession number Z49205), HEL cells (accession number U42030), bovine endothelium (accession numberX87628), rat cells (accession numbers U22830 and U22829), turkey brain (accession number U09842) and chicken brain (accession number X73268).
  • SEQ ID NO:16 The following sequence for the P2Y1 receptor is derived from H.sapiens (accession number S81950).
  • SEQ ID NO:17 The following sequence for the P2Y2 receptor is derived from H.sapiens epithelial cells (accession number U07225). Other sequences have been published for P2Y2 receptors from rat alveolar cells (accession number U09402), rat pituitary cells (accession number L46865), Wistar Kyoto rat (accession number U56839), and mouse neuroblastoma cells (accession number NM_008773).
  • SEQ ID NO:18 The following sequence for the P2Y2 receptor is derived from H.sapiens epithelial cells (accession number U07225) protein sequence.
  • SEQ ID NO:19 The following sequence for the P2y3 receptor is derived from chick brain (accession number X98283).
  • SEQ ID NO:20 The following sequence for the P2y3 receptor is derived from chick brain (accession number X98283) protein sequence.
  • SEQ ID NO:21 The following sequence for the P2Y4 receptor is derived from H.sapiens (accession number X91852). Other sequences have been published for P2Y4 receptors from human chromosome X (accession number U40223), and rat heart (accession number Y14705).
  • SEQ ID NO:22 The following sequence for the P2Y4 receptor is derived from H.sapiens (accession number X91852) Protein sequence.
  • SEQ ID NO:23 The following sequence for the P2Y6 receptor is derived from H.sapiens placenta (accession numberX97058). Other sequences have been published for P2Y6 receptors from human placenta (accession number AF007893), and human activated T-cells (accession number U52464).
  • SEQ ID NO:22 The following sequence for the P2Y6 receptor is derived from H.sapiens (accession number X91852) Protein sequence.
  • SEQ ID NO:24 The following sequence for the P2Y11 receptor is derived from human placenta (accession number AF030335). Other sequences have been published for P2Y11 receptors from human HL-60 cells (accession number AJ298334).
  • the following sequence for the P2Y11 receptor is derived from human placenta (accession number AF030335) protein sequence.

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